ExampleTrees

A set of Ig lineage trees generated from the <code>ExampleDb</code> file, subset to
only those trees with at least four nodes.

datasets

Provides methods for high-throughput adaptive immune
receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In
particular, immunoglobulin (Ig) sequence lineage reconstruction,
lineage topology analysis, diversity profiling, amino acid property
analysis and gene usage.
Citations:
Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>,
Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.

Susanna Marquez

alakazam

Immunoglobulin Clonal Lineage and Diversity Analysis

Namita Gupta

Nima Nouri

Ruoyi Jiang

Julian Zhou

Kenneth Hoehn

Daniel Gadala-Maria

Edel Aron

Cole Jensen

Gisela Gabernet

Caroline Sullivan

Hailong Meng

Burhan Sabuwala

Jason Vander Heiden

Steven Kleinstein

ExampleTrees function

A list of igraph objects output by buildPhylipLineage.
 Each node of each tree has the following annotations (vertex attributes):<ul>
<li><code>sample_id</code>: Sample identifier(s). Time in relation to vaccination.</li>
<li><code>c_call</code>: Isotype assignment(s).</li>
<li><code>duplication_count</code>: Copy count (number of duplicates) of the sequence.</li>
</ul>

Format

Example Ig lineage trees — ExampleTrees

Example Ig lineage trees

ExampleTrees: Example Ig lineage trees

Description

Usage

Arguments

Format

See Also